Question: Quality Assessment of RNA de novo assemble (trinity) without reference genome
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gravatar for sdbaney
4 weeks ago by
sdbaney10
sdbaney10 wrote:

Hello, Are there any tools within the galaxy tool shed that would give me a quality assessment of my trinity assembly without using a reference genome (as there is none for my organism)? I ran two assemblies with the same data trimmed with different parameters and I am trying to figure out a way to determine which one yielded a better assembly. Unfortunately, all of the quality assessment tools uses a reference genome to map the transcripts back to it which I don't have.

trinity illumina qa rna-seq • 85 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by sdbaney10
0
gravatar for sdbaney
4 weeks ago by
sdbaney10
sdbaney10 wrote:

I ended up finding a command line program called transrate that runs metrics on the assemblies without a reference genome. It is working very well. Wanted to give an update.

ADD COMMENTlink written 4 weeks ago by sdbaney10
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